The National Defense Authorization Act for Fiscal Year 2012 runs hundreds of pages. It authorizes hundreds of billions in defense spending. And as it stands, the version of the bill approved by the Senate is facing a veto by President Obama.

The administration's main objection is to one part of the bill, the part that governs the treatment of detainees. According to the administration's reading of it, the bill mandates military custody for a certain class of terrorism suspects. And since it would apply to individuals inside the U.S., it would, and this is a quote, "be inconsistent with the fundamental American principle that our military does not patrol our streets."

Well, John Brennan is President Obama's chief counterterrorism adviser, and he joins us from the White House. Welcome.

JOHN BRENNAN: Hi, Robert.

SIEGEL: The administration says the detainee provisions here could restrict intelligence professionals from doing their job and restrict the president's ability to fight terrorism. How exactly would it do that?

BRENNAN: Well, in a number of ways. First of all, we don't believe that this legislation is necessary from the standpoint of the language that is included on detainees and military detention. What it calls for is that there'd be required military detention for certain individuals who are determined to be part of al-Qaida, and that would apply whether or not these individuals are captured overseas or, you know, captured, arrested here in the United States.

And so, what we've tried to do in this administration is to maintain as much flexibility as possible. And anything that restricts our flexibility in terms of how we want to detain them, question them, prosecute them is something that counterterrorism professionals and practitioners really are very concerned about.

SIEGEL: But is the administration's concern here based on the efficacy of making cases, investigating terrorist suspects? Or is it over the principle that the military doesn't enforce law in the U.S.?

BRENNAN: Well, it's both. One is that it complicates greatly the ability of individuals who capture these individuals or arrest them to make the determinations in the immediate aftermath of that detention, about how to handle them. And so, that puts quite frankly a lot of red tape. And the last thing that we need in government is more red tape.

Secondly, we have, I think, a very strong established track record of dealing successfully with individuals here in the United States who are involved in terrorism-related activities. President Obama, I think, has a record second to none in terms of his willingness and determination to go after these individuals aggressively overseas, but also to deal with them forcefully if they're found here the United States.

SIEGEL: But it seems that part of what you're up against here is some pretty broad public resistance to treating terror plots as common felonies. This is what Republican Senator Lindsey Graham of South Carolina said when he took issue with those who claim that this law violates the prohibition against a military role in law enforcement.

SENATOR LINDSEY GRAHAM: This is the central difference between us. I don't believe fighting al-Qaida is a law enforcement function. I believe our military should be deeply involved in fighting these guys at home and abroad.

BRENNAN: Yeah. Well, I don't agree with Senator Graham. I, you know, I think that they are well-intentioned in terms of what they're going to do. But the practitioners who are out there really want to make sure that we're able to deal with these individuals appropriately. They're not considered to be common criminals.

What we want to do is to extract the intelligence from them so that we can keep this country safe. We cannot hamper this effort. It's been successful to date and this legislation really puts that at risk.

SIEGEL: Now, there's criticism from the other side as well. Some civil libertarians are very concerned that this bill would permit a U.S. citizen to be detained indefinitely by the military. In addressing that concern, Senator Carl Levin of Michigan quoted the Hamdi decision, which said that a citizen, no less than an alien, can be part of supporting forces hostile to the U.S., and there is no bar to this nation's holding one of its own citizens as an enemy combatant.

For the administration, is the inclusion of U.S. citizens picked up on U.S. soil at all troubling here?

BRENNAN: It is very troubling in terms of picking up somebody here on U.S. soil. If there are U.S. citizens who are engaged in hostilities on the battlefield abroad, we want to make sure that our military is able to deal with them appropriately. But there also are certain considerations we need to account for in terms of U.S. citizenship.

We are a country that takes very seriously our commitment to the rule of law. When I go overseas and I talk to other governments, talking to them about making sure that they handle their cases appropriately and not throw people into military detention, not throw them into a military court, hold them indefinitely without the due process of law, this is what has caused a lot of problems overseas. And if we go down this road, we're sending a very bad signal.

We need to demonstrate, through the strength of our judicial system, that we can handle these issues, particularly on our soil, in a way that's consistent with our commitment to that rule of law, but also works very effectively in terms of getting the intelligence we need to keep this country safe.

SIEGEL: Senator Dianne Feinstein of California attached an amendment to the bill which says: Nothing in this section shall be construed to affect existing law or authorities relating to the detention of United States citizens, lawful resident aliens of the U.S., or any other persons who are captured or arrested in the United States.

If that language isn't sufficient to satisfy the administration and win the signature of the president, what is? What would be sufficient?

BRENNAN: Well, you know, we've looked at the latest versions of the legislation and it's still insufficient. And the president has made it clear he is not going to sign any piece of legislation that restricts his ability to deal effectively with the terrorist threat we face. And so, there are a number of recommendations that have been put forward to ensure that we are able to continue to prosecute our effort.

You know, Senator Feinstein and others have been, I think, working very strongly to try to get some of this language in there that will protect our citizenship, our liberties and our freedom.

SIEGEL: Well, Mr. Brennan, thank you very much for talking with us today.

BRENNAN: Thank you. Thank you.

SIEGEL: John Brennan, who is deputy national security adviser for Homeland Security and Counterterrorism, and assistant to the president. He is President Obama's chief adviser on counterterrorism. Transcript provided by NPR, Copyright NPR.